Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005117.1 Hibiscus syriacus cultivar Beakdansim tig00011504_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129754
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:219 original size:17 final size:18
Alignment explanation
Indices: 172--220 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
162 AATGGTTTTT
*
172 ATATCATATGTTTATTTA
1 ATATCATATGTTTATTAA
190 ATA-C-TATTGGTTT-TTAA
1 ATATCATA-T-GTTTATTAA
207 ATATCATATGTTTA
1 ATATCATATGTTTA
221 ATTTTAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 9 0.36
19 2 0.08
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (18 bp):
ATATCATATGTTTATTAA
Found at i:267 original size:38 final size:37
Alignment explanation
Indices: 164--267 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 37
154 AATTATAAAA
164 TGGTTTTT--ATATCATATGTTT-A-TTTAATACTAT
1 TGGTTTTTAAATATCATATGTTTAATTTTAATACTAT
197 TGGTTTTTAAATATCATATGTTTAATTTTAATACTA-
1 TGGTTTTTAAATATCATATGTTTAATTTTAATACTAT
*
233 TGGTTTTTAAAATATCATGTCGTTTAATTTTAATA
1 TGGTTTTT-AAATATCATAT-GTTTAATTTTAATA
268 TTAATACTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
33 8 0.12
35 13 0.20
36 9 0.14
37 20 0.31
38 14 0.22
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.54
Consensus pattern (37 bp):
TGGTTTTTAAATATCATATGTTTAATTTTAATACTAT
Found at i:946 original size:33 final size:33
Alignment explanation
Indices: 902--964 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
892 GGAGTATCGG
*
902 TACTCCTTTAATAAGTATCG-TACTCCATTACGA
1 TACTCCATTAATAA-TATCGATACTCCATTACGA
*
935 TACTCCATTAATGATATCGATACTCCATTA
1 TACTCCATTAATAATATCGATACTCCATTA
965 ATGAGTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (33 bp):
TACTCCATTAATAATATCGATACTCCATTACGA
Found at i:1000 original size:21 final size:21
Alignment explanation
Indices: 932--994 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
922 TACTCCATTA
932 CGATACTCCATTAATGA-TAT
1 CGATACTCCATTAATGAGTAT
952 CGATACTCCATTAATGAGTAT
1 CGATACTCCATTAATGAGTAT
*
973 CGATACTCCTTTAATGAGTAT
1 CGATACTCCATTAATGAGTAT
994 C
1 C
995 ATTACTACCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (21 bp):
CGATACTCCATTAATGAGTAT
Found at i:4823 original size:20 final size:21
Alignment explanation
Indices: 4773--4831 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
4763 CAGAACCCCA
**
4773 GGGGGTATCGATTCCCTTGTG
1 GGGGGTATCGATTCCCTCATG
* *
4794 GGGGGAATCGGTTCCCTCAT-
1 GGGGGTATCGATTCCCTCATG
4814 GGGGGTATCGATTCCCTC
1 GGGGGTATCGATTCCCTC
4832 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.12, C:0.24, G:0.36, T:0.29
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTCATG
Found at i:12528 original size:16 final size:16
Alignment explanation
Indices: 12507--12561 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
12497 AGTCACATAT
12507 ATAATTTAGACGAAAA
1 ATAATTTAGACGAAAA
12523 ATAATTTA-A--AAATA
1 ATAATTTAGACGAAA-A
12537 TATAATTTAGACGAAAA
1 -ATAATTTAGACGAAAA
12554 ATAATTTA
1 ATAATTTA
12562 AAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 9 0.26
16 17 0.50
17 1 0.03
18 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATTTAGACGAAAA
Found at i:12538 original size:31 final size:31
Alignment explanation
Indices: 12503--12574 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
12493 ATTTAGTCAC
12503 ATATATAATTTAGACGAAAAATAATTTAAAA
1 ATATATAATTTAGACGAAAAATAATTTAAAA
12534 ATATATAATTTAGACGAAAAATAATTTAAAA
1 ATATATAATTTAGACGAAAAATAATTTAAAA
12565 ATATATAATT
1 ATATATAATT
12575 GTTTGTTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.35
Consensus pattern (31 bp):
ATATATAATTTAGACGAAAAATAATTTAAAA
Found at i:12543 original size:15 final size:15
Alignment explanation
Indices: 12523--12574 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
12513 TAGACGAAAA
12523 ATAATTTAAAAATAT
1 ATAATTTAAAAATAT
12538 ATAATTTAGACGAAA-A-
1 ATAATTTA-A--AAATAT
12554 ATAATTTAAAAATAT
1 ATAATTTAAAAATAT
12569 ATAATT
1 ATAATT
12575 GTTTGTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 15 0.47
16 9 0.28
17 1 0.03
18 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (15 bp):
ATAATTTAAAAATAT
Found at i:13355 original size:3 final size:3
Alignment explanation
Indices: 13342--13388 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
13332 GATTGATGGG
13342 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13389 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15480 original size:18 final size:18
Alignment explanation
Indices: 15459--15506 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
15449 CGTTTTTCTT
15459 TTTCTTTTAATTTCATCC
1 TTTCTTTTAATTTCATCC
* ** *
15477 TTTCCTTT-ATTTTTTTC
1 TTTCTTTTAATTTCATCC
15494 TTTCTTTTAATTT
1 TTTCTTTTAATTT
15507 ACATTTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTTAATTTCATCC
Found at i:19092 original size:7 final size:7
Alignment explanation
Indices: 19076--19131 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
19066 CAATCATAAC
19076 AAAAAG-
1 AAAAAGA
19082 AAAAAGA
1 AAAAAGA
19089 AAAAA-A
1 AAAAAGA
*
19095 ACAAAGA
1 AAAAAGA
19102 AAAAAGA
1 AAAAAGA
*
19109 AAAGAGA
1 AAAAAGA
19116 AAATAA-A
1 AAA-AAGA
*
19123 AAAGAGA
1 AAAAAGA
19130 AA
1 AA
19132 CAAAAACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
6 12 0.29
7 28 0.68
8 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:19100 original size:19 final size:19
Alignment explanation
Indices: 19078--19147 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 19
19068 ATCATAACAA
19078 AAAGAAAAAGAAAAAAAAC
1 AAAGAAAAAGAAAAAAAAC
19097 AAAGAAAAAAGAAAAGAGAAA-
1 AAAG-AAAAAGAAAA-A-AAAC
19118 ATAA-AAAAGAGAAACAAAAAC
1 A-AAGAAAA-AGAAA-AAAAAC
19139 AAAGGAAAA
1 AAA-GAAAA
19148 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
19 4 0.10
20 19 0.45
21 9 0.21
22 10 0.24
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAAAAC
Found at i:19105 original size:14 final size:13
Alignment explanation
Indices: 19076--19147 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
19066 CAATCATAAC
*
19076 AAAAAGAAAAAGA
1 AAAAAAAAAAAGA
*
19089 AAAAAAACAAAGA
1 AAAAAAAAAAAGA
*
19102 AAAAAGAAAAGAGA
1 AAAAA-AAAAAAGA
*
19116 AAATAAAAAAGAGA
1 AAA-AAAAAAAAGA
*
19130 AACAAAAACAAAGGA
1 AA-AAAAA-AAAAGA
19145 AAA
1 AAA
19148 TGTGAAGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
13 16 0.33
14 24 0.49
15 9 0.18
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:19110 original size:26 final size:26
Alignment explanation
Indices: 19076--19127 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
19066 CAATCATAAC
19076 AAAAAGAAAA-AGAAAAAAAACAAAGA
1 AAAAAGAAAAGAGAAAAAAAA-AAAGA
*
19102 AAAAAGAAAAGAGAAAATAAAAAAGA
1 AAAAAGAAAAGAGAAAAAAAAAAAGA
19128 GAAACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAGAGAAAAAAAAAAAGA
Found at i:20239 original size:32 final size:32
Alignment explanation
Indices: 20203--20276 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
20193 AGGAACAATT
* *
20203 GGGCATCTTTAAAGATTTAACATCAAATGTTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
* ** *
20235 GGGCATTTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
20267 GGGCATCTTT
1 GGGCATCTTT
20277 GGGAATTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
GGGCATCTTTAAAGATTCAACATCAAATATTG
Found at i:20572 original size:64 final size:64
Alignment explanation
Indices: 20469--20761 Score: 376
Period size: 64 Copynumber: 4.6 Consensus size: 64
20459 CAGCTTTTAG
** *
20469 AGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTCAA
1 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAA
* * * * * * * *
20533 AGTCAATTTCAACCTCACAGA-GAATGATGTTGGATTCAACAAATAACTTTCTAGTTTTATTCAG
1 AGTCAATTTCAACTTCACA-ACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAA
* *
20597 AGTCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATT-AG
1 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTC-ATTCAA
* * *
20661 AGTCAATTTTAACTTCACAACGAAGGATATTGGACTCGACAAACAACTTTCTAGTTTCATTCAGA
1 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCA-A
* *
20726 A-TCAATTTCAATTTCACATCGAAGGATATTGGACTC
1 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
20762 GAAACAATGC
Statistics
Matches: 200, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
63 4 0.02
64 192 0.96
65 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (64 bp):
AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAA
Found at i:20703 original size:128 final size:128
Alignment explanation
Indices: 20467--20761 Score: 414
Period size: 128 Copynumber: 2.3 Consensus size: 128
20457 TGCAGCTTTT
** *
20467 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTCA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCA
* * * * *
20532 AAGTCAATTTCAACCTCACAGAGAATGATGTTGGATTCAACAAATAACTTTCTAGTTTTATTC
66 AAGTCAATTTCAACCTCACAGAGAAGGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
*
20595 AGAGTCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATT-
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTC-ATTC
* * * *
20659 AGAGTCAATTTTAACTTCACA-ACGAAGGATATTGGACTCGACAAACAACTTTCTAGTTTCATTC
65 AAAGTCAATTTCAACCTCACAGA-GAAGGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
* * *
20723 AGAATCAATTTCAATTTCACATCGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
20762 GAAACAATGC
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
127 1 0.01
128 144 0.97
129 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (128 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCA
AAGTCAATTTCAACCTCACAGAGAAGGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
Found at i:21046 original size:124 final size:124
Alignment explanation
Indices: 20845--21194 Score: 524
Period size: 124 Copynumber: 2.8 Consensus size: 124
20835 GAAACAATCC
* * *
20845 TTGGATTTCAACTTCACAACGAAGGATAT-CAACT-AAAGGTTCAACTTCACAATGAATGAGCCA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA-GCTCAACTTCACAACGAATGAGCCA
* *
20908 TCCACGATTTCAACTTCACGACGAAGGATATCATGCCCACAAGCAGCATCCATCTCTAGA
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGA
* * * *
20968 TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAGGAGTCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
21033 CCACGATTTCAACTTCATGATGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGA
* * *
21092 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAACTAAACTTCACGACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * *
21157 CCACAATTTCAATTTCACAACGAAGGATATCGTGCCCA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
21195 ACGGATCGAC
Statistics
Matches: 202, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
123 28 0.14
124 171 0.85
125 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGA
Found at i:21543 original size:86 final size:86
Alignment explanation
Indices: 21257--22008 Score: 811
Period size: 86 Copynumber: 8.8 Consensus size: 86
21247 CCTAGCCAAG
* * * * * *
21257 TACATCATAACTCAAGGCGAGAATGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACATTT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
21321 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * *
21342 TACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACTTTCGAGTTTGATTAAATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
*
21406 AGCT-AAAGGCATATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * * **
21426 CATAACATAACTCAAGGCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTACATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
21491 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * * * * *
21512 TACATCATAGCTCAAGGAGAGAAAGACTATCTGTCAACAAAAGTCCTTCGAGTTTGATTACACTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
* *
21577 AGCTCACAGGCACATCGAATT
66 AGCTCAAAGGCACATCAAATT
* * * * * * *
21598 TATAGCATAGCTTAAGGCGAGAAAGACTATCTGTCAAGAAAA-AGCCTTCGAGTTCGATTACACT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGA-CCTTCGAGTTCGATTACATT
* *
21662 CAGCTCAAATGCATATCAAATT
65 CAGCTCAAAGGCACATCAAATT
* * * * * *
21684 TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAAC-TAAGACCTTCGAGTTCAATTACACTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
21748 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * *
21769 TACAACATAGGTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAATTCGATTATATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
* * * *
21834 ATCTCAGAGGCATATCAACTT
66 AGCTCAAAGGCACATCAAATT
* * * * * *
21855 TACATCATAGCTCAAGACGATAAGGGCTATTTCTCAATC-AAA-ACCTTCGAGTTCGATTCCATT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAAGACCTTCGAGTTCGATTACATT
* * **
21918 CACCTCAAGGGCATGTCAAATT
65 CAGCTCAAAGGCACATCAAATT
* * * * ** * **
21940 CACAGCATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAAATGTT-GAGTTCGATT-CTATT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTAC-ATT
22003 CAGCTC
65 CAGCTC
22009 GTCGATACAT
Statistics
Matches: 559, Mismatches: 99, Indels: 18
0.83 0.15 0.03
Matches are distributed among these distances:
84 48 0.09
85 245 0.44
86 265 0.47
87 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (86 bp):
TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
AGCTCAAAGGCACATCAAATT
Found at i:21819 original size:171 final size:171
Alignment explanation
Indices: 21262--22008 Score: 831
Period size: 171 Copynumber: 4.4 Consensus size: 171
21252 CCAAGTACAT
* * * * *
21262 CATAACTCAAGGCGAGAATGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACATTTAGCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* *
21326 AAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACTTTCG
66 AAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCG
* * * * *
21391 AGTTTGATTAAATTCAGCT-AAAGGCATATCAAATTCATAA
131 AGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAA
* * * **
21431 CATAACTCAAGGCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * *
21496 AAAGGCACATCAAATTTACATCATAGCTCAAGGAGAGAAAGACTATCTGTCAACAAAAGTCCTTC
66 AAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTC
* * * * * *
21561 GAGTTTGATTACACTCAGCTCACAGGCACATCGAATTTATAG
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAA
* * * *
21603 CATAGCTTAAGGCGAGAAAGACTATCTGTCAAGAAAA-AGCCTTCGAGTTCGATTACACTCAGCT
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGA-CCTTCGAGTTCGATTACATTCAGCT
* * * * * * *
21667 CAAATGCATATCAAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACTAAGACCTTC
65 CAAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTC
* *
21732 GAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTACAA
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAA
* * * * *
21774 CATAGGTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAATTCGATTATATTCATCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * * * * *
21839 AGAGGCATATCAACTTTACATCATAGCTCAAGACGATAAGGGCTATTTCTCAATCAAA-ACCTTC
66 AAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAGACCTTC
* * * * ** *
21903 GAGTTCGATTCCATTCACCTCAAGGGCATGTCAAATTCACAG
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAA
* * * * **
21945 CATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAAATGTT-GAGTTCGATT-CTATTCAGCT
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTAC-ATTCAGCT
22008 C
65 C
22009 GTCGATACAT
Statistics
Matches: 487, Mismatches: 84, Indels: 13
0.83 0.14 0.02
Matches are distributed among these distances:
169 30 0.06
170 96 0.20
171 241 0.49
172 120 0.25
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (171 bp):
CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
AAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCG
AGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAA
Found at i:22665 original size:17 final size:17
Alignment explanation
Indices: 22630--22665 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
22620 TTCATTATTT
*
22630 ATTATGTATCAGGTCCA
1 ATTATGTATCAGATCCA
*
22647 ATTATGTATCAGATTCA
1 ATTATGTATCAGATCCA
22664 AT
1 AT
22666 AAAAGGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (17 bp):
ATTATGTATCAGATCCA
Found at i:23776 original size:16 final size:15
Alignment explanation
Indices: 23755--23796 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
23745 TACGTTTTGA
23755 TTAATTTTTTTAAAT
1 TTAATTTTTTTAAAT
**
23770 TTAAATTTAATTAAAT
1 TT-AATTTTTTTAAAT
23786 TTAATTTTTTT
1 TTAATTTTTTT
23797 CTTTCTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAATTTTTTTAAAT
Found at i:24538 original size:20 final size:20
Alignment explanation
Indices: 24498--24707 Score: 217
Period size: 20 Copynumber: 10.3 Consensus size: 20
24488 CTGACTATAA
*
24498 CAACGAGTATCCGTAAAATCG
1 CAACGCGTATCCGT-AAATCG
24519 CAACGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
* *
24539 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
24560 CAACGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
** * *
24580 CAACAAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
* *
24600 CAACGTGTATCTGTAAATCG
1 CAACGCGTATCCGTAAATCG
* * *
24620 CAACGAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
* *
24640 CAATGCGTATCCGTAAATCA
1 CAACGCGTATCCGTAAATCG
* *
24660 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
24681 CAACGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
24701 CAACGCG
1 CAACGCG
24708 ATTTTTAAAG
Statistics
Matches: 154, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
20 108 0.70
21 46 0.30
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAACGCGTATCCGTAAATCG
Found at i:24542 original size:81 final size:81
Alignment explanation
Indices: 24452--24708 Score: 297
Period size: 81 Copynumber: 3.2 Consensus size: 81
24442 GCGAATATGA
* * * * *
24452 AAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTATAACAACGAGTATCCGTAAA
1 AAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-AATCACAACGAGAATACGTAAA
24515 ATCGCAACGCGTATCCGT
64 ATCGCAACGCGTATCCGT
* * * *
24533 AAATCGCAACGACAATACGTA-AAATCGCAACGCGTATCCGTAAATCGCAACAAGAATACGT-AA
1 AAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAA
* *
24596 ATCGCAACGTGTATCTGT
64 ATCGCAACGCGTATCCGT
* * ** * *
24614 AAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCACAACGACAATACGTAAAAT
1 AAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAAAT
24679 CGCAACGCGTATCCGT
66 CGCAACGCGTATCCGT
24695 AAATCGCAACGCGA
1 AAATCGCAACGCGA
24709 TTTTTAAAGC
Statistics
Matches: 146, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 37 0.25
81 71 0.49
82 28 0.19
83 8 0.05
84 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAAAT
CGCAACGCGTATCCGT
Found at i:24543 original size:41 final size:41
Alignment explanation
Indices: 24498--24705 Score: 321
Period size: 41 Copynumber: 5.1 Consensus size: 41
24488 CTGACTATAA
* *
24498 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
24539 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* * *
24580 CAACAAGAATACGT-AAATCGCAACGTGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
24620 CAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCA
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
24660 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
24701 CAACG
1 CAACG
24706 CGATTTTTAA
Statistics
Matches: 151, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 72 0.48
41 79 0.52
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:24610 original size:40 final size:41
Alignment explanation
Indices: 24509--24705 Score: 317
Period size: 40 Copynumber: 4.9 Consensus size: 41
24499 AACGAGTATC
24509 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* *
24550 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACAAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* * *
24591 CGT-AAATCGCAACGTGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* *
24631 CGT-AAATCGCAATGCGTATCCGTAAATCACAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
24671 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
24706 CGATTTTTAA
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 72 0.50
41 71 0.50
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
Found at i:25306 original size:21 final size:21
Alignment explanation
Indices: 25280--25339 Score: 88
Period size: 19 Copynumber: 3.0 Consensus size: 21
25270 CACAACATGA
25280 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
* *
25301 AAATGAAAATCGCGAC--GCG
1 AAATGAAAATCGCAACGAGAG
25320 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
25340 TAATCGCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.50, C:0.17, G:0.23, T:0.10
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:25324 original size:19 final size:20
Alignment explanation
Indices: 25265--25339 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
25255 TTCTAAACTT
*
25265 AAAATCACAACATGA-AAATG
1 AAAATCGCAACA-GAGAAATG
25285 AAAATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGAGAAATG
* *
25306 AAAATCGCGAC-GCGAAATG
1 AAAATCGCAACAGAGAAATG
25325 AAAATCGCAAC-GAGA
1 AAAATCGCAACAGAGA
25340 TAATCGCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
19 20 0.42
20 12 0.25
21 16 0.33
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACAGAGAAATG
Found at i:25409 original size:33 final size:33
Alignment explanation
Indices: 25367--25488 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
25357 CAAAATCGCA
25367 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
*
25400 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
** *
25433 TTGCGATAGTCATTTCCGCATTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTT--G-T-G--ATTCTCTCG
25473 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
25489 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 45 0.60
34 5 0.07
36 1 0.01
38 1 0.01
39 1 0.01
40 22 0.29
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
Found at i:25486 original size:20 final size:20
Alignment explanation
Indices: 25424--25479 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
25414 TCGCGTTGCG
25424 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
25444 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATAGTC
25464 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
25480 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.75
21 2 0.06
22 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:27345 original size:94 final size:94
Alignment explanation
Indices: 27184--27563 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
27174 TAGATTGCTT
* * *
27184 AGTAAATTTATTCGGTTTCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
27249 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
27278 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
27343 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
27372 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
27437 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * **
27466 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCCGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
27531 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
27559 AGTAA
1 AGTAA
27564 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 10, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 249 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:27743 original size:19 final size:19
Alignment explanation
Indices: 27698--27734 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27688 ACGAGAAATG
27698 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
27717 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
27735 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:27803 original size:20 final size:20
Alignment explanation
Indices: 27778--27864 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
27768 GATTCTCTCG
**
27778 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
27798 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
27818 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
27838 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
27858 TTGCGAT
1 TTGCGAT
27865 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:28439 original size:21 final size:21
Alignment explanation
Indices: 28348--28452 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
28338 GACTCACCTG
* *
28348 TCATCGTTCAAGTGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
28370 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
28390 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
28411 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
28432 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
28453 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:28445 original size:42 final size:42
Alignment explanation
Indices: 28373--28455 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
28363 CCTCCCCTAT
*
28373 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
28415 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
28456 ACATTCTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:29828 original size:14 final size:14
Alignment explanation
Indices: 29809--29844 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29799 ATTGTTTAAT
29809 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
29823 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
29837 TGATTTGT
1 TGATTTGT
29845 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30003 original size:33 final size:35
Alignment explanation
Indices: 29966--30035 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 35
29956 GAAAATGACT
29966 ATCGCAACGAG-AGAATCGCAATGCG-AAA-TGAAA
1 ATCGCAACGAGTA-AATCGCAATGCGAAAATTGAAA
29999 ATCGCAACGAGTAAATCGCAATGCGAAAATTGAAA
1 ATCGCAACGAGTAAATCGCAATGCGAAAATTGAAA
30034 AT
1 AT
30036 TAAATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 23 0.68
34 4 0.12
35 7 0.21
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (35 bp):
ATCGCAACGAGTAAATCGCAATGCGAAAATTGAAA
Found at i:32370 original size:24 final size:24
Alignment explanation
Indices: 32336--32389 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32326 CTGAAAAATC
32336 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
32360 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
32384 ATCAAA
1 ATCAAA
32390 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:32403 original size:24 final size:24
Alignment explanation
Indices: 32336--32403 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
32326 CTGAAAAATC
* * *
32336 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
32360 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
32384 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
32404 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:33322 original size:20 final size:20
Alignment explanation
Indices: 33251--33336 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
33241 CAGATTCTCG
*
33251 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTAATCGCA
* * *
33271 TTACGATTTACGTATTCGTA
1 TTGCGATTTACGTAATCGCA
33291 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
33311 TTGCGATTTACGTAATCGCG
1 TTGCGATTTACGTAATCGCA
33331 TTGCGA
1 TTGCGA
33337 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.02
20 58 0.98
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:33357 original size:21 final size:21
Alignment explanation
Indices: 33333--33378 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33323 TAATCGCGTT
33333 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
33354 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
33375 GCGA
1 GCGA
33379 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:33452 original size:20 final size:20
Alignment explanation
Indices: 33429--33642 Score: 225
Period size: 20 Copynumber: 10.6 Consensus size: 20
33419 TACCGGAGAT
33429 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33449 CGCGTTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
33469 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
33490 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
33510 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
33530 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
33550 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33570 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
33590 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
33611 CGCGTTGTGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
33632 CTCGTTGCGAT
1 CGCGTTGCGAT
33643 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 106 0.67
21 52 0.33
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33637 original size:41 final size:41
Alignment explanation
Indices: 33431--33642 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
33421 CCGGAGATCG
* *
33431 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
33472 CGTTGTGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
33512 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
33552 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
33593 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
33634 CGTTGCGAT
1 CGTTGCGAT
33643 AGTCAGAATC
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 75 0.48
41 82 0.52
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:33674 original size:20 final size:20
Alignment explanation
Indices: 33651--33703 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
33641 ATAGTCAGAA
*
33651 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
33671 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
33691 TCGCGTTGCGATT
1 TCGCGTTGCGATT
33704 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:33695 original size:40 final size:40
Alignment explanation
Indices: 33431--33703 Score: 214
Period size: 40 Copynumber: 6.8 Consensus size: 40
33421 CCGGAGATCG
* * * *
33431 CGTTGCGATTTACGGATACGCGTTGTGATTT-TACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTATA--TGTTCT
* * * ** *
33472 CGTTGTGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTATATGTTCT
** *
33512 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTATATGTTCT
* * *
33552 CGTTGCGATTTACGGATACGCGTTGCGATTT-TACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTATA--TGTTCT
* * * *
33593 CGTTGCGATTTACGGATACGCGTTGTGATTT-TACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTATA-TG-TTCT
* *
33634 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTATATGTTCT
* * *
33674 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
33704 CTGGAAAATC
Statistics
Matches: 195, Mismatches: 28, Indels: 19
0.81 0.12 0.08
Matches are distributed among these distances:
39 1 0.01
40 99 0.51
41 92 0.47
42 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTATATGTTCT
Found at i:33696 original size:81 final size:81
Alignment explanation
Indices: 33428--33703 Score: 308
Period size: 81 Copynumber: 3.4 Consensus size: 81
33418 ATACCGGAGA
* * * *
33428 TCGCGTTGCGATTTACGGATACGCGTTGTGATTTTACGTATTGTCGTTGTGATTTACGGATACGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* ** *
33493 ATTGCGATTTACGTAT
66 GTTGCGATTTATATGT
*
33509 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
*
33573 GTTGCGATTT-TACGT
66 GTTGCGATTTATATGT
* * * * * * *
33588 ATTGTCGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 -TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA
33651 TCGCGTTGCGATTTATATGT
63 -CGCGTTGCGATTTATATGT
* * *
33671 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATT
33704 CTGGAAAATC
Statistics
Matches: 164, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.01
80 41 0.25
81 80 0.49
82 37 0.23
83 5 0.03
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (81 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
GTTGCGATTTATATGT
Found at i:33802 original size:20 final size:19
Alignment explanation
Indices: 33753--33806 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
33743 ATTCTTCATA
33753 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
33772 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
33793 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
33807 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:37462 original size:21 final size:22
Alignment explanation
Indices: 37426--37466 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
37416 GGTTGCGGAA
*
37426 TTGATGGTGTTTGATGATGAAG
1 TTGATGGCGTTTGATGATGAAG
37448 TTGATGGCG-TTGATGATGA
1 TTGATGGCGTTTGATGATGA
37467 GAAGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.02, G:0.37, T:0.39
Consensus pattern (22 bp):
TTGATGGCGTTTGATGATGAAG
Found at i:39389 original size:23 final size:23
Alignment explanation
Indices: 39363--39420 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
39353 CACCACAGCT
*
39363 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
39386 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
39409 CGTAGAATTGCA
1 CGTAGAATTGCA
39421 TCGTAGTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:40119 original size:63 final size:65
Alignment explanation
Indices: 40024--40165 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 65
40014 AATGGAGGTA
* ** *
40024 TGCATCGATGCACTACACCATGCATCGATGCATAAATAATATTCGATGTTTGTA-TTTAATGGGG
1 TGCATCGATGCACTACACCATGCATCGATGCATAAATAACATTCGATGTTTGTATTTTAAAAGAG
* ** **
40088 TGCATCGATGCACT-C-CTTATGCATCGATGCATCTATGGCATTCGATGTTTGTATTTTAAAAGA
1 TGCATCGATGCACTACAC-CATGCATCGATGCATAAATAACATTCGATGTTTGTATTTTAAAAGA
40151 G
65 G
40152 TGCATCGATGCACT
1 TGCATCGATGCACT
40166 TCATGTGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 1 0.01
63 31 0.46
64 35 0.52
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (65 bp):
TGCATCGATGCACTACACCATGCATCGATGCATAAATAACATTCGATGTTTGTATTTTAAAAGAG
Found at i:42176 original size:210 final size:211
Alignment explanation
Indices: 41582--42394 Score: 1224
Period size: 210 Copynumber: 3.8 Consensus size: 211
41572 ATTTAAGAAT
41582 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A--AG
**
41647 GGATCAAATTGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAATAA--ACTAAATTATA
62 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAA-AAGTACTAAATTATA
* * * * *
41710 CCCATTTAAAAAGTTATGGGCTAATTAAAAAAATTGAATTAAGTAATAAGTATGGATTAATTTCA
126 CCCATTTAAAAAGTTATGGGCCAATTAAAAATA-T-AAATAAGTAATAAGTATGGGTCAATTTCA
*
41775 TATGCAAATAAAATTTGGAGGAC
189 GATGCAAATAAAATTTGGAGGAC
*
41798 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-AAGGG
* *
41863 ATCAAATCTAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
64 ATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
*
41928 ATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATG
129 ATTTAAAAAGTTATGGGCCAA-TTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGATG
*
41993 CAAATAAAATTCGGAGGAC
193 CAAATAAAATTTGGAGGAC
* *
42012 TAAATTGAACAAATATGAAATTACAAATAAAAATTTTAATATATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* *
42075 CAAATCAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
* *
42140 TTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGTAATAAGTATGAGTCAATTTCAGGTGCA
131 TTAAAAAGTTATGGGCCAA-TTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
*
42205 AATAAAATTTGGAGAAC
195 AATAAAATTTGGAGGAC
* *
42222 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAAGACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* * * *
42285 CAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAAATATACTCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
* *
42350 TAAAAAAGTTATGAGCCAATTAATAAATATAAATAAGTAATAAGT
131 TTAAAAAGTTATGGGCCAATTAA-AAATATAAATAAGTAATAAGT
42395 TGAGAAAAAA
Statistics
Matches: 561, Mismatches: 32, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
209 4 0.01
210 304 0.54
213 3 0.01
214 147 0.26
215 34 0.06
216 69 0.12
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
ATAAAATTTGGAGGAC
Found at i:42423 original size:2 final size:2
Alignment explanation
Indices: 42418--42526 Score: 91
Period size: 2 Copynumber: 54.5 Consensus size: 2
42408 AAAACAACTA
*
42418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
42460 AT AT GT AT -T AT AT AT AT AT ACT AT AT AGT TT TT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * *
42502 AT GT AT AA AGT AT AA AT -T AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT A
42527 CCATGTATAA
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
1 4 0.05
2 78 0.90
3 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42532 original size:27 final size:27
Alignment explanation
Indices: 42491--42543 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
42481 TATATAGTTT
** *
42491 TTATATATATTATGTATAAAGTATAAA
1 TTATATATACCATGTATAAACTATAAA
42518 TTATATATACCATGTATAAACTATAA
1 TTATATATACCATGTATAAACTATAA
42544 TACTTTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (27 bp):
TTATATATACCATGTATAAACTATAAA
Found at i:42646 original size:17 final size:17
Alignment explanation
Indices: 42626--42719 Score: 66
Period size: 17 Copynumber: 5.3 Consensus size: 17
42616 CTATACAATT
* *
42626 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
42643 TATAATTATAAATAATA
1 TATATTTATAAATTATA
42660 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
42678 TAGTTTATTGATATAAATTATA
1 TA---TATT--TATAAATTATA
* *
42700 TA-GTTTATATA-TATA
1 TATATTTATAAATTATA
42715 TATAT
1 TATAT
42720 AGTATATATG
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
15 6 0.10
16 6 0.10
17 18 0.30
18 14 0.23
21 4 0.07
22 13 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:42695 original size:22 final size:22
Alignment explanation
Indices: 42662--42722 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
42652 AAATAATATA
42662 TATTG-TATAAATTATATAGTT
1 TATTGATATAAATTATATAGTT
42683 TATTGATATAAATTATATAGTT
1 TATTGATATAAATTATATAGTT
*
42705 TA-T-ATATATA-TATATAGT
1 TATTGATATAAATTATATAGT
42723 ATATATGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 6 0.16
22 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (22 bp):
TATTGATATAAATTATATAGTT
Found at i:42739 original size:7 final size:7
Alignment explanation
Indices: 42729--42762 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
42719 TAGTATATAT
42729 GGTTTAG
1 GGTTTAG
42736 GGTTTAG
1 GGTTTAG
*
42743 GGTTTAA
1 GGTTTAG
*
42750 TGTTTAG
1 GGTTTAG
42757 GGTTTA
1 GGTTTA
42763 TATTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:42770 original size:6 final size:6
Alignment explanation
Indices: 42759--42783 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42749 ATGTTTAGGG
42759 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
42784 AAACTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:42808 original size:14 final size:13
Alignment explanation
Indices: 42791--42845 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
42781 TATAAACTAC
42791 ATACTATAATTTAT
1 ATACTAT-ATTTAT
42805 ATACTATATTT-T
1 ATACTATATTTAT
42817 ATACTAT-TTATAT
1 ATACTATATT-TAT
*
42830 AAACTATAGTTTAT
1 ATACTATA-TTTAT
42844 AT
1 AT
42846 TTATATACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 2 0.06
12 9 0.26
13 11 0.31
14 11 0.31
15 2 0.06
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (13 bp):
ATACTATATTTAT
Found at i:42862 original size:33 final size:33
Alignment explanation
Indices: 42809--42894 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
42799 ATTTATATAC
*
42809 TATATTTTATACTATTTATATA-AACTATAGTT
1 TATATTTTATACTATATATATACAACTATAGTT
42841 TATATTTATATACTATATATATACGAACTATAGTT
1 TATATTT-TATACTATATATATAC-AACTATAGTT
* * *
42876 TACATATGA-ACTATATATA
1 TATATTTTATACTATATATA
42895 AAAATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 7 0.15
33 24 0.51
34 1 0.02
35 15 0.32
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (33 bp):
TATATTTTATACTATATATATACAACTATAGTT
Found at i:42974 original size:43 final size:42
Alignment explanation
Indices: 42928--43082 Score: 223
Period size: 43 Copynumber: 3.8 Consensus size: 42
42918 TGATATTTAT
42928 ATATGAACTATAGTTTACATATAAACTATATAGTTTATATAC
1 ATATGAACTATAGTTTACATATAAACTATATAGTTTATATAC
42970 TATATGAACTATAGTTTACATATAAACTATATAGTTTATATAC
1 -ATATGAACTATAGTTTACATATAAACTATATAGTTTATATAC
*
43013 ---T-AACTATAGTTTACATATAAAC--TATAGTTAATATTTAC
1 ATATGAACTATAGTTTACATATAAACTATATAGTT--TATATAC
*
43051 ATATGAACTATAGTTTACATATGAACTATATA
1 ATATGAACTATAGTTTACATATAAACTATATA
43083 TATAAACTAT
Statistics
Matches: 102, Mismatches: 2, Indels: 15
0.86 0.02 0.13
Matches are distributed among these distances:
36 7 0.07
38 27 0.26
39 1 0.01
41 1 0.01
42 20 0.20
43 42 0.41
44 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (42 bp):
ATATGAACTATAGTTTACATATAAACTATATAGTTTATATAC
Found at i:43091 original size:31 final size:32
Alignment explanation
Indices: 43051--43119 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
43041 TAATATTTAC
*
43051 ATATGAAC-TATAGTTTACATATGAACTATAT
1 ATATAAACATATAGTTTACATATGAACTATAT
*
43082 ATATAAACTATATAGTTTACATATGAGCTATAT
1 ATATAAAC-ATATAGTTTACATATGAACTATAT
43115 ATATA
1 ATATA
43120 TATATACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 7 0.21
33 27 0.79
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (32 bp):
ATATAAACATATAGTTTACATATGAACTATAT
Found at i:43112 original size:20 final size:20
Alignment explanation
Indices: 42923--43115 Score: 121
Period size: 18 Copynumber: 9.9 Consensus size: 20
42913 AAGGTTGATA
*
42923 TTTATATATGAAC--TATAG
1 TTTACATATGAACTATATAG
*
42941 TTTACATATAAACTATATAG
1 TTTACATATGAACTATATAG
42961 TTTATATACTATATGAAC--TATAG
1 --T-T-TAC-ATATGAACTATATAG
*
42984 TTTACATATAAACTATATAG
1 TTTACATATGAACTATATAG
*
43004 TTTATATACT-AAC--TATAG
1 TTTACATA-TGAACTATATAG
* *
43022 TTTACATATAAACTATAGTTAATA
1 TTTACATATGAACTATA--T-A-G
43046 TTTACATATGAAC--TATAG
1 TTTACATATGAACTATATAG
43064 TTTACATATGAACTATATA-
1 TTTACATATGAACTATATAG
43083 --T--ATA--AACTATATAG
1 TTTACATATGAACTATATAG
*
43097 TTTACATATGAGCTATATA
1 TTTACATATGAACTATATA
43116 TATATATATA
Statistics
Matches: 139, Mismatches: 10, Indels: 50
0.70 0.05 0.25
Matches are distributed among these distances:
13 9 0.06
15 3 0.02
16 1 0.01
17 2 0.01
18 49 0.35
19 4 0.03
20 36 0.26
21 2 0.01
22 4 0.03
23 7 0.05
24 15 0.11
25 7 0.05
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTACATATGAACTATATAG
Found at i:43169 original size:20 final size:19
Alignment explanation
Indices: 42936--43172 Score: 108
Period size: 20 Copynumber: 12.2 Consensus size: 19
42926 ATATATGAAC
42936 TATAGTTTACATATAAACTA
1 TATAGTTTACATAT-AACTA
*
42956 TATAGTTTATATACTATA-TGAA
1 TATAGTTTACATA-TA-ACT--A
42978 CTATAGTTTACATATAAACTA
1 -TATAGTTTACATAT-AACTA
*
42999 TATAGTTTATATACTAAC--
1 TATAGTTTACATA-TAACTA
43017 TATAGTTTACATATAAACTA
1 TATAGTTTACATAT-AACTA
*
43037 TAGTTAATATTTACATATGAAC--
1 TA--T-A-GTTTACATAT-AACTA
43059 TATAGTTTACATATGAACTA
1 TATAGTTTACATAT-AACTA
43079 TATA---T--ATA-AACTA
1 TATAGTTTACATATAACTA
*
43092 TATAGTTTACATATGAGCTA
1 TATAGTTTACATAT-AACTA
* *
43112 TATA-TATATATAT-AC--
1 TATAGTTTACATATAACTA
**
43127 TATAGTTGATATTTATATACTA
1 TATAGTT--TACATATA-ACTA
*
43149 TATAGTTTACATATGACCTA
1 TATAGTTTACATAT-AACTA
43169 TATA
1 TATA
43173 TATATACTAT
Statistics
Matches: 169, Mismatches: 16, Indels: 64
0.68 0.06 0.26
Matches are distributed among these distances:
13 9 0.05
15 7 0.04
16 2 0.01
17 3 0.02
18 37 0.22
19 8 0.05
20 58 0.34
21 5 0.03
22 13 0.08
23 15 0.09
24 12 0.07
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (19 bp):
TATAGTTTACATATAACTA
Found at i:43194 original size:53 final size:52
Alignment explanation
Indices: 43077--43244 Score: 180
Period size: 53 Copynumber: 3.2 Consensus size: 52
43067 ACATATGAAC
* * *
43077 TATATATATAAACTATATAGTTTACATATGAGCTATATATATATATATACTATAGT
1 TATATTTATATACTATATAGTTTACATATGA-C---CTATATATATATACTATAGT
43133 TGATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGCT
1 T-ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAG-T
* * * * *
43187 TATATTTATATATTATATATTTTATATATAAACTATATATA-AT-CTATAG-
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGT
43236 TATAATTTA
1 TAT-ATTTA
43245 CATATGAACT
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
49 3 0.03
50 5 0.05
51 6 0.06
52 2 0.02
53 53 0.52
54 2 0.02
56 2 0.02
57 28 0.28
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (52 bp):
TATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGT
Found at i:43224 original size:20 final size:19
Alignment explanation
Indices: 42920--43226 Score: 94
Period size: 20 Copynumber: 16.2 Consensus size: 19
42910 ACTAAGGTTG
*
42920 ATATTTATATATGAACTAT
1 ATATTTATATATAAACTAT
* *
42939 A-GTTTACATATAAACTAT
1 ATATTTATATATAAACTAT
42957 ATAGTTTATATACTATATGAACTAT
1 ATA--TT-TATA-TATA--AACTAT
* *
42982 A-GTTTACATATAAACTAT
1 ATATTTATATATAAACTAT
43000 ATAGTTTATATACT-AACTAT
1 ATA-TTTATATA-TAAACTAT
* *
43020 A-GTTTACATATAAACTATAGTT
1 ATATTTATATATAAAC--TA--T
* *
43042 AATATTTACATATGAACTAT
1 -ATATTTATATATAAACTAT
* * *
43062 A-GTTTACATATGAAC---
1 ATATTTATATATAAACTAT
43077 -TA--TATATATAAACTAT
1 ATATTTATATATAAACTAT
* * *
43093 ATAGTTTACATATGAGCTAT
1 ATA-TTTATATATAAACTAT
*
43113 ATA--TATATATATACTAT
1 ATATTTATATATAAACTAT
* * *
43130 AGT-TGATATTTATATACTAT
1 A-TAT-TTATATATAAACTAT
* * *
43150 ATAGTTTACATATGACCTAT
1 ATA-TTTATATATAAACTAT
* *
43170 ATATATATACTAT-AGCT-T
1 ATATTTATA-TATAAACTAT
*
43188 ATATTTATATAT-TA-TAT
1 ATATTTATATATAAACTAT
43205 AT-TTTATATATAAACTAT
1 ATATTTATATATAAACTAT
43223 ATAT
1 ATAT
43227 AATCTATAGT
Statistics
Matches: 214, Mismatches: 38, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
13 9 0.04
16 10 0.05
17 21 0.10
18 60 0.28
19 11 0.05
20 64 0.30
21 7 0.03
22 8 0.04
23 5 0.02
24 12 0.06
25 7 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATTTATATATAAACTAT
Found at i:43228 original size:11 final size:11
Alignment explanation
Indices: 43209--43263 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
43199 TTATATATTT
43209 TATATATAAAC
1 TATATATAAAC
*
43220 TATATATAATC
1 TATATATAAAC
**
43231 TATAGTATAATT
1 TATA-TATAAAC
* *
43243 TACATATGAAC
1 TATATATAAAC
43254 TATATATAAA
1 TATATATAAA
43264 AATCCTAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (11 bp):
TATATATAAAC
Found at i:43314 original size:33 final size:33
Alignment explanation
Indices: 43276--43432 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 33
43266 TCCTAAACCC
43276 TAAACTATACATTATATAGT-TTATTAGTATATA
1 TAAACTATACATTATATA-TATTATTAGTATATA
* * *
43309 TAAACTATATAATATATATATACTATATGGTATATA
1 TAAACTATA-CAT-TATATATATTAT-TAGTATATA
43345 TAAACTATACATTATATATAATTCATTAGTATATA
1 TAAACTATACATTATATAT-ATT-ATTAGTATATA
* *
43380 TAAACTATATATTATATAGT-TCATTAGTATATA
1 TAAACTATACATTATATA-TATTATTAGTATATA
* *
43413 TAAACTATATAGTATATATA
1 TAAACTATACATTATATATA
43433 AACAATATAT
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
32 1 0.01
33 37 0.35
34 11 0.10
35 38 0.36
36 20 0.19
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (33 bp):
TAAACTATACATTATATATATTATTAGTATATA
Found at i:43326 original size:18 final size:18
Alignment explanation
Indices: 43300--43441 Score: 143
Period size: 18 Copynumber: 8.1 Consensus size: 18
43290 TATAGTTTAT
43300 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
43318 TAATATATATATACTATA
1 TAGTATATATAAACTATA
*
43336 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * *
43354 CATTATATAT-AATTCAT-
1 TAGTATATATAAACT-ATA
43371 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
**
43389 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
43404 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
43422 TAGTATATATAAACAATA
1 TAGTATATATAAACTATA
43440 TA
1 TA
43442 TTAATTTATT
Statistics
Matches: 99, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
15 4 0.04
16 8 0.08
17 21 0.21
18 66 0.67
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:43388 original size:26 final size:29
Alignment explanation
Indices: 43357--43423 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 29
43347 AACTATACAT
*
43357 TATATATAATTCATTAGTATATATAAACTATA
1 TATATATAGTTCATTAGTATATATAAAC---A
43389 TATTATATAGTTCATTAGTATATATAAAC-
1 TA-TATATAGTTCATTAGTATATATAAACA
43418 TATATA
1 TATATA
43424 GTATATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.12
29 2 0.06
32 2 0.06
33 25 0.76
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (29 bp):
TATATATAGTTCATTAGTATATATAAACA
Found at i:43485 original size:26 final size:26
Alignment explanation
Indices: 43428--43494 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
43418 TATATAGTAT
* **
43428 ATATAAACA-ATATATTAATTTATTA
1 ATATAAACATATATATTAATTAAAGA
43453 ATATAAACATATATATTAATTGAAAGA
1 ATATAAACATATATATTAATT-AAAGA
*
43480 AT-TAAAAAATATATA
1 ATAT-AAACATATATA
43495 AGGATCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.26
26 12 0.34
27 14 0.40
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (26 bp):
ATATAAACATATATATTAATTAAAGA
Found at i:43493 original size:104 final size:104
Alignment explanation
Indices: 43281--43494 Score: 238
Period size: 104 Copynumber: 2.1 Consensus size: 104
43271 AACCCTAAAC
* * * * *
43281 TATACATTATATAGTTTATTAGTATATATAAACTATATAATATATATATACTATATGGTATATAT
1 TATATATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAACAATATAGTATATAT
* * * * *
43346 AAACTATACATTATATATAATTCATTAGTATATATAAAC
66 AAACTAAACATTATATATAATTCATAAGAATATAAAAAA
* * *
43385 TATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAACAATATATTAATTTA
1 TATATATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAACAATATAGT-ATATA
*
43450 TTAATA-TAAACA-TATATATTAATTGA-AAGAAT-TAAAAAA
65 -TAA-ACTAAACATTATATA-TAATTCATAAGAATATAAAAAA
43489 TATATA
1 TATATA
43495 AGGATCAAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
104 63 0.68
105 14 0.15
106 14 0.15
107 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (104 bp):
TATATATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAACAATATAGTATATAT
AAACTAAACATTATATATAATTCATAAGAATATAAAAAA
Found at i:43582 original size:61 final size:61
Alignment explanation
Indices: 43496--43630 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 61
43486 AAATATATAA
* * * *
43496 GGATCAAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATCATAA-CATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCA-AATCATTAAATTT
* * *
43557 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATTATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTT
* *
43618 AGACTAAATTGAA
1 GGATTAAATTGAA
43631 TAAATTTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 2 0.03
61 62 0.97
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (61 bp):
GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTT
Found at i:46370 original size:19 final size:19
Alignment explanation
Indices: 46346--46382 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46336 ACATCATAAG
46346 TTAAAAACTTATAATTTTA
1 TTAAAAACTTATAATTTTA
*
46365 TTAAAATCTTATAATTTT
1 TTAAAAACTTATAATTTT
46383 GTCCATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAACTTATAATTTTA
Found at i:46671 original size:32 final size:32
Alignment explanation
Indices: 46630--46692 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
46620 TCTAAATCGG
* *
46630 GTTCAGGTCAACATCAGTTCCGACTCGAGTCT
1 GTTCAGGTCAAAAACAGTTCCGACTCGAGTCT
**
46662 GTTCAGGTCAAAAACAGTTTTGACTCGAGTC
1 GTTCAGGTCAAAAACAGTTCCGACTCGAGTC
46693 GGTTTCAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (32 bp):
GTTCAGGTCAAAAACAGTTCCGACTCGAGTCT
Found at i:48982 original size:18 final size:18
Alignment explanation
Indices: 48939--48995 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 18
48929 CTTTTCTTAT
48939 TTTTCTTTTCTTTTTGTC
1 TTTTCTTTTCTTTTTGTC
*
48957 TGAATTTTTTCTTCTTTTTGTC
1 T---TTTCTT-TTCTTTTTGTC
48979 TTTTCTTTTCTTTTTGT
1 TTTTCTTTTCTTTTTGT
48996 ACTCTAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
21 5 0.15
22 12 0.36
ACGTcount: A:0.04, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTC
Found at i:49304 original size:15 final size:15
Alignment explanation
Indices: 49284--49328 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
49274 TATAGATGGC
49284 TGCGGAATTGATAGT
1 TGCGGAATTGATAGT
49299 TGCGGAATTGATAGT
1 TGCGGAATTGATAGT
*
49314 TGCAGAATTGATAGT
1 TGCGGAATTGATAGT
49329 GTTTGATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (15 bp):
TGCGGAATTGATAGT
Found at i:49361 original size:21 final size:22
Alignment explanation
Indices: 49321--49361 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
49311 AGTTGCAGAA
*
49321 TTGATAGTGTTTGATGATGAAG
1 TTGATAGTGTTTGATAATGAAG
49343 TTGATAGTG-TTGATAATGA
1 TTGATAGTGTTTGATAATGA
49362 GAAGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (22 bp):
TTGATAGTGTTTGATAATGAAG
Found at i:51062 original size:39 final size:39
Alignment explanation
Indices: 51008--51106 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 39
50998 AAACGATGAG
*
51008 GAAAATGGTGAATTAGGGATTGAGATGCGAA-AGAGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGC-AAGAGAGAAAT
* *
51047 GAAAATGGGGAATTAGGGATTGAGGTGCAAGAGGGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGCAAGAGAGAAAT
51086 GAAAATGGGGAATTAGGGATT
1 GAAAATGGGGAATTAGGGATT
51107 TTAGCAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 2 0.04
39 54 0.96
ACGTcount: A:0.40, C:0.02, G:0.37, T:0.20
Consensus pattern (39 bp):
GAAAATGGGGAATTAGGGATTGAGATGCAAGAGAGAAAT
Found at i:55122 original size:2 final size:2
Alignment explanation
Indices: 55061--55113 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
55051 TTTATGTATC
55061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55103 TA TA TA TA TA T
1 TA TA TA TA TA T
55114 GGATATATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55312 original size:24 final size:24
Alignment explanation
Indices: 55265--55313 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
55255 ATGTAATCTA
55265 ATATAATATACACTTACATAAAAAT
1 ATATAATATACAC-TACATAAAAAT
55290 ATATGAATATACA-TACATGAAAAA
1 ATAT-AATATACACTACAT-AAAAA
55314 AATAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATATAATATACACTACATAAAAAT
Found at i:56559 original size:3 final size:3
Alignment explanation
Indices: 56551--56622 Score: 110
Period size: 3 Copynumber: 23.3 Consensus size: 3
56541 CTACAAAAGC
56551 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
56599 AAGT AAT AAT AAT AAT AAAT AAT A
1 AA-T AAT AAT AAT AAT -AAT AAT A
56623 TTTTTTCAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.02
3 57 0.88
4 7 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56842 original size:43 final size:42
Alignment explanation
Indices: 56784--57030 Score: 130
Period size: 40 Copynumber: 5.7 Consensus size: 42
56774 GTGGGGAGAC
* * *
56784 GACATGGCTCATACGTGATGAAGAGTTTTGGTCATCTAAGGGT
1 GACAAGGCTCATACGTGATGAAGAGTTCTAGTCATC-AAGGGT
* * * *
56827 GACAAGGCTCCTACGTGATGATGAGATCTAGTCAAGCAA---T
1 GACAAGGCTCATACGTGATGAAGAGTTCTAGTC-ATCAAGGGT
** *
56867 GACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGT
1 GACAAGGCTCATACGTGATGAAGAGTTC-TAGTCATC------AAGGGT
** * *
56916 GATAACACTGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTT
1 G---ACAAGGCTCATACGTGATGAAGAGTTCTAGTCATCAAGGG-T
* * * *
56962 GACAAGGCTCCTACGTGATGAGGAGATCT-G--GT-AAGGTGAT
1 GACAAGGCTCATACGTGATGAAGAGTTCTAGTCATCAAGG-G-T
**
57002 GACACTGCTCATACGTGATGAAGAGTTCT
1 GACAAGGCTCATACGTGATGAAGAGTTCT
57031 TGGCCATCTT
Statistics
Matches: 159, Mismatches: 29, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
39 4 0.03
40 53 0.33
41 4 0.03
42 1 0.01
43 52 0.33
44 2 0.01
45 5 0.03
46 4 0.03
49 2 0.01
51 5 0.03
52 27 0.17
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
GACAAGGCTCATACGTGATGAAGAGTTCTAGTCATCAAGGGT
Found at i:56946 original size:52 final size:50
Alignment explanation
Indices: 56868--57082 Score: 160
Period size: 52 Copynumber: 4.6 Consensus size: 50
56858 TCAAGCAATG
56868 ACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATA
1 ACACTGCTCATACGTGATGAAGAGTTCTTAG--ATCTTTAGGAAGGGTGATA
* ** *
56920 ACACTGCTCATACGTGATGAAGAGTTC-T-G---GTTATCAAGGGT--TG
1 ACACTGCTCATACGTGATGAAGAGTTCTTAGATCTTTAGGAAGGGTGATA
** * *
56963 ACAAGGCTCCTACGTGATG-AG-G-----AGATC--T-GGTAA-GGTGATG
1 ACACTGCTCATACGTGATGAAGAGTTCTTAGATCTTTAGG-AAGGGTGATA
* *
57003 ACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGAAAGGGTGATA
1 ACACTGCTCATACGTGATGAAGAGTTCTTAG--ATCTTTAGGAAGGGTGATA
*
57055 ACACTGCTCATACGTGATAAAGAGTTCT
1 ACACTGCTCATACGTGATGAAGAGTTCT
57083 GGTTATCAAG
Statistics
Matches: 127, Mismatches: 16, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
38 4 0.03
39 3 0.02
40 18 0.14
41 3 0.02
42 3 0.02
43 17 0.13
45 9 0.07
47 1 0.01
49 3 0.02
50 1 0.01
51 4 0.03
52 61 0.48
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (50 bp):
ACACTGCTCATACGTGATGAAGAGTTCTTAGATCTTTAGGAAGGGTGATA
Found at i:57037 original size:135 final size:134
Alignment explanation
Indices: 56790--57276 Score: 607
Period size: 135 Copynumber: 3.7 Consensus size: 134
56780 AGACGACATG
* * *
56790 GCTCATACGTGATGAAGAGTTTTGGTCATCTAAGGG-TGACAAGGCTCCTACGTGATGATGAGAT
1 GCTCATACGTGATGAAGAGTTCTGGTTATC-AAGGGTTGACAAGGCTCCTACGTGATGAGGAGAT
* **
56854 CTAGTCAA-GCAATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGA
65 CTGGT-AAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTA-GAAGGGTGA
56918 TAACACT
128 TAACACT
56925 GCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACGTGATGAGGAGATC
1 GCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACGTGATGAGGAGATC
*
56990 TGGTAAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGAAAGGGTGATA
66 TGGTAAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAG-AAGGGTGATA
57055 ACACT
130 ACACT
* * *
57060 GCTCATACGTGATAAAGAGTTCTGGTTATCAAGGGTTGACACGACTCCTACGTGATGAGGAGATC
1 GCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACGTGATGAGGAGATC
* * * * *
57125 TGGTCAGGTGATGACACGGCTCATATGTGATGAAGAGTTC-TAGCCATC--TA-AA-TGAGATAA
66 TGGTAAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGAAGGGTGATAA
* *
57185 TATT
131 CACT
* * * * * * * *
57189 GTTCCTACGTGATGAGGACG-ACTGGTTATC-TGGGTTGACACA-GCTCCTACATAATGAAGAGA
1 GCTCATACGTGATGAAGA-GTTCTGGTTATCAAGGGTTGACA-AGGCTCCTACGTGATGAGGAGA
* *
57251 TCTGGTCAGGTGATGACACTACTCAT
64 TCTGGTAAGGTGATGACACTGCTCAT
57277 CTGTTCATGA
Statistics
Matches: 316, Mismatches: 31, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
128 49 0.16
129 31 0.10
130 3 0.01
132 2 0.01
134 15 0.05
135 216 0.68
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (134 bp):
GCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACGTGATGAGGAGATC
TGGTAAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGAAGGGTGATAA
CACT
Found at i:57400 original size:88 final size:87
Alignment explanation
Indices: 57295--57471 Score: 282
Period size: 88 Copynumber: 2.0 Consensus size: 87
57285 GAGTCTTGGC
* * *
57295 CATCTAAGGTGACAACACGGTTCCACACTGATGGGGACGGCTGGTTATCTAATTTGACACAGCTC
1 CATCTAAGGTGACAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCTC
57360 CTACATAATGAGGAAATCTGGT
66 CTACATAATGAGGAAATCTGGT
* * *
57382 CATCTAAAGGTGATAACACGGTTCCACTCTAATGGGGACGACTGGTTATCTAAGTTGACACATCT
1 CATCT-AAGGTGACAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCT
*
57447 CCTACATAATGAGGAGATCTGGT
65 CCTACATAATGAGGAAATCTGGT
57470 CA
1 CA
57472 GGTGATTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 5 0.06
88 77 0.94
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
CATCTAAGGTGACAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCTC
CTACATAATGAGGAAATCTGGT
Found at i:57805 original size:32 final size:32
Alignment explanation
Indices: 57737--57808 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
57727 CATCAGGATG
* * * * * *
57737 TTGAATCCCCGAAGATGCCTCAATATTTGATG
1 TTGAATCTCCAAAGATACCTCAACATTCGATA
*
57769 TTGAATCTCCAAAGATACCTCAACATTCGCTA
1 TTGAATCTCCAAAGATACCTCAACATTCGATA
57801 TTGAATCT
1 TTGAATCT
57809 TTAAATATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGAATCTCCAAAGATACCTCAACATTCGATA
Found at i:67162 original size:2 final size:2
Alignment explanation
Indices: 67089--67153 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
67079 TTTATGTATC
67089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67131 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
67154 GCATATATAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71952 original size:21 final size:21
Alignment explanation
Indices: 71905--71953 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
71895 CTTAAGCGAT
* *
71905 ATCAAACTACTTATTACTTGA
1 ATCAACCTACTTATCACTTGA
71926 ATCAACCTACTTATCACTTGA
1 ATCAACCTACTTATCACTTGA
71947 ATCAACC
1 ATCAACC
71954 CTCGTTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (21 bp):
ATCAACCTACTTATCACTTGA
Found at i:74191 original size:24 final size:26
Alignment explanation
Indices: 74164--74229 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 26
74154 GAAAATAAAA
74164 AAAACAATAAAATAATAAT-GAAA-T-
1 AAAA-AATAAAATAATAATAGAAAGTC
74188 AAAAAATTAAAATAATAATAGAAAGTC
1 AAAAAA-TAAAATAATAATAGAAAGTC
*
74215 AAATGAATAAAATAA
1 AAA-AAATAAAATAA
74230 AAAAAGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 2 0.06
24 16 0.44
25 4 0.11
26 1 0.03
27 11 0.31
28 2 0.06
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAAAATAAAATAATAATAGAAAGTC
Found at i:75840 original size:34 final size:34
Alignment explanation
Indices: 75736--75857 Score: 158
Period size: 33 Copynumber: 3.6 Consensus size: 34
75726 CTTGAGGGTC
* *
75736 TTTGTGTTTTAAGAGATAC-ATTTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGG--TTTT
*
75772 TTTATGTTTCAAGAGAAACGATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
75805 TTTGCGTTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
75839 TTTGTGCTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
75858 TGTCTCTAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
33 31 0.40
34 20 0.26
36 25 0.32
37 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.42
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:75961 original size:37 final size:36
Alignment explanation
Indices: 75910--76186 Score: 254
Period size: 37 Copynumber: 7.8 Consensus size: 36
75900 CAAAGGTTGG
*
75910 TGTTTCAATAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
75947 TGTTTCAAGGGAAACTGTCTCAAGAGACACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
75983 TGTTTGAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
76020 AGTTCCAAAAGAAACTGTCCCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
76056 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
76085 TGTTTCAAGGGAAACTGTCTCAAGAGATAC-AAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
76120 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
76157 TGTTT--TGAGTAAATTAGTCTCAAGAGAGAC
1 TGTTTCAAGAG-AAACT-GTCTCAAGAGAGAC
76187 GCCCCTTTGT
Statistics
Matches: 196, Mismatches: 29, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
31 1 0.01
32 1 0.01
33 2 0.01
35 35 0.18
36 53 0.27
37 82 0.42
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:76003 original size:73 final size:72
Alignment explanation
Indices: 75910--76161 Score: 281
Period size: 73 Copynumber: 3.6 Consensus size: 72
75900 CAAAGGTTGG
*
75910 TGTTTCAATAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAC
75975 ACAAAATT
66 AC-AAATT
* * * ** * * *
75983 TGTTTGAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAC
76048 ACGAAATT
66 AC-AAATT
* *
76056 TGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
*
76111 ATACAAATT
64 ACACAAATT
*
76120 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
76162 TGAGTAAATT
Statistics
Matches: 144, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
63 2 0.01
64 20 0.14
65 28 0.19
67 2 0.01
70 2 0.01
71 1 0.01
72 10 0.07
73 77 0.53
74 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAC
ACAAATT
Found at i:78150 original size:38 final size:38
Alignment explanation
Indices: 78089--78178 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 38
78079 CATATGAAAA
* * * *
78089 GTCCTACGGGACACAGATTACATCCTTCGGGATGACAG
1 GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
*
78127 GTCCTTCGGGACATAGATGACATCCTTCGAGATGATAG
1 GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
*
78165 GTCCTTCGGAACAT
1 GTCCTTCGGGACAT
78179 TTATACGAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (38 bp):
GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
Found at i:79016 original size:76 final size:77
Alignment explanation
Indices: 78908--79105 Score: 276
Period size: 76 Copynumber: 2.6 Consensus size: 77
78898 GTTGTACAAG
* * * * *
78908 GGGGGGAATCAGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
**
78971 AAAAACTGTTTA
66 AAAAACCATTTA
* *
78983 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
*
79048 CAAAACCATTTA
66 AAAAACCATTTA
*
79060 GGGGGG-ATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
79106 ATCTGTAATT
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
75 17 0.15
76 78 0.71
77 15 0.14
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (77 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
AAAAACCATTTA
Found at i:81698 original size:21 final size:21
Alignment explanation
Indices: 81672--81752 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
81662 CAGAACCCCA
*
81672 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
81693 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* *
81716 AGGGGGAATCGGTT-CCCTCA-
1 GGGGGGAATCGATTCCCCT-AT
*
81736 GGGGGGGATCGATTCCC
1 GGGGGGAATCGATTCCC
81753 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:87702 original size:77 final size:77
Alignment explanation
Indices: 87510--87714 Score: 265
Period size: 76 Copynumber: 2.7 Consensus size: 77
87500 CCGTTGTACA
* * * * *
87510 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCAGTTCCCTCCGAGCATACTGGAATTCTCAGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
**
87573 GAAAAACTGTTT
66 GAAAAACCATTT
* *
87585 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
*
87649 GCCAAAACCATTT
66 G-AAAAACCATTT
* *
87662 AGGGGGG-ATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTG
87715 TAATTTTTGG
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
75 25 0.22
76 46 0.40
77 43 0.38
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
GAAAAACCATTT
Found at i:90150 original size:22 final size:22
Alignment explanation
Indices: 90125--90172 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
90115 TTTTCTTCAC
*
90125 TTTTTCCTTTGT-TTTTGTTTCT
1 TTTTTCCTTTCTCTTTT-TTTCT
*
90147 TTTTTCTTTTCTCTTTTTTTCT
1 TTTTTCCTTTCTCTTTTTTTCT
90169 TTTT
1 TTTT
90173 GTTCTGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTCCTTTCTCTTTTTTTCT
Found at i:92083 original size:15 final size:17
Alignment explanation
Indices: 92063--92096 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
92053 TGCAAGTGAT
92063 GAAAATAA-AA-GAAAA
1 GAAAATAATAATGAAAA
92078 GAAAATAATAATGAAAA
1 GAAAATAATAATGAAAA
92095 GA
1 GA
92097 GTTAGTGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
GAAAATAATAATGAAAA
Found at i:93233 original size:5 final size:5
Alignment explanation
Indices: 93223--93316 Score: 56
Period size: 5 Copynumber: 19.0 Consensus size: 5
93213 AGTTAGTAAA
* *
93223 AAAAT AAAAT AAACA- AAAAT --AAT AAAAT AATAAT GAAAT AAAA- AAATT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT
* * *
93271 AAAAT AATAAT AGAAAGT CAAAT -GAAT AAAAT AAAA- AAAGT AAAAT
1 AAAAT AA-AAT A-AAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
93317 GGTTAGTTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
3 3 0.04
4 10 0.14
5 40 0.58
6 14 0.20
7 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:95983 original size:26 final size:26
Alignment explanation
Indices: 95952--96003 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
95942 GGATTATGCA
*
95952 CTTTATACTGTCCTGAAGCATATTAT
1 CTTTATACTGCCCTGAAGCATATTAT
95978 CTTTATACTGCCCTGAAGCATATTAT
1 CTTTATACTGCCCTGAAGCATATTAT
96004 GCTTCTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (26 bp):
CTTTATACTGCCCTGAAGCATATTAT
Found at i:100226 original size:14 final size:14
Alignment explanation
Indices: 100207--100245 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
100197 TTTTCATTTG
100207 TTCTTCCCCTTCGC
1 TTCTTCCCCTTCGC
100221 TTCTTCCCCTTCGC
1 TTCTTCCCCTTCGC
100235 TTCTTCCCCTT
1 TTCTTCCCCTT
100246 ACAGATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.00, C:0.49, G:0.05, T:0.46
Consensus pattern (14 bp):
TTCTTCCCCTTCGC
Found at i:106025 original size:19 final size:19
Alignment explanation
Indices: 105990--106027 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
105980 GTAAAACTAT
*
105990 TTTTATTATATTATATTTA
1 TTTTATTATAATATATTTA
106009 TTTTATATATAAT-TATTTA
1 TTTTAT-TATAATATATTTA
106028 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATTATAATATATTTA
Found at i:109037 original size:23 final size:23
Alignment explanation
Indices: 109010--109056 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
109000 AATACCAAAG
*
109010 ATAAA-TATAAATCTACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
109033 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
109056 A
1 A
109057 CAACCCCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:129336 original size:15 final size:15
Alignment explanation
Indices: 129316--129345 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
129306 ATTAACCTGT
129316 AGTTAATCTTCTATC
1 AGTTAATCTTCTATC
*
129331 AGTTAATTTTCTATC
1 AGTTAATCTTCTATC
129346 CCAGCTCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
AGTTAATCTTCTATC
Done.